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TITAN S/TEM (FEI), 300kV
OPERATION MANUAL for Basic TEM

Overview.
TITAN is a 300kV high resolution Transmission Electron Microscope (TEM). The microscopes
interface contains three parts: the TEM Server, User Interface (UI), and control-panels (left and
right). The sophisticated software that controls the entire microscope is called the TEM Server.
Because the functionality of the TEM Server is vital to the Titan, the TEM Server is not
accessible to ordinary users. Users communicate with the TEM Server (and therefore with the
microscope) via the User Interface (UI), which is basically a second-level program. The UI
provides access to the necessary microscope functions. Knobs and buttons in the control panels
imitate the usual TEM controls but in reality they interact with the computer, which in turn
controls every function of the microscope. The extent of control depends on the position of the
user in FEIs user-account hierarchy: factory service supervisor user. Users have
enough control to operate the microscope in all possible modalities, but are limited in ability to
corrupt vital Titan settings, adjustments, etc. Every user has his or her own standard Windows
account protected by password. Every new account inherits the supervisor settings at the time it is
created. Later the settings can be altered and saved by the user under his/her account. Also, users
may load other users settings at any time, including the supervisors the advantage of digital
interface.

The control panels contain a standard set of TEM controls: intensity (brightness), magnification, focus, focus-step,
dark field, diffraction, wobbler, stage X-Y joystick, user beam shift trackball, Z-height and multifunction knobs X and
Y (MF). The MF knobs default function is user beam shift X & Y. However, they can also be bind to other
functions such as beam tilt, astigmatism correction, etc. The current function of the MF knobs is shown in the UI
Binding window. Sensitivity of some knobs may be adjusted using the and +buttons located just above. There is
also a set of user-defined buttons (programmable buttons) that function as switches. The user may assign (bind) these
buttons to frequently used functions such as screen lift, spotsize etc. MF knobs and programmable buttons may be
bound to many microscope functions and therefore provide flexibility and convenience in microscope operation.

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The User Interface (UI) links the microscope Control panels to the TEM server and therefore
functions as the microscope interface:
The UI contains a number of panels and windows. They are arranged in an L-shape around a central empty space
(black, above). The central space is reserved for additional programs like TIA, Digital Micrograph, etc. The
horizontal, bottom part of the UI contains mostly information windows: Message window, Status window with
current microscope parameters etc.
The vertical part of the UI contains numerous Control panels that control different microscope parameters.
Every Control panel contains a set of controls related to a main microscope function such as FEG (Field Emission
Gun) control, Stage control (CompuStage), Camera control, etc. All of these Control panels are organized in a
Workset and may be called up by choosing the corresponding tab at the top. Flap-outs are used to extend the list
of available options/choices on some Control panels. The Workset contains frequently used microscope controls and
mainly functions as an organizer for the Control panels. The list of all accessible microscope controls is available
through the Popup panel at the bottom-right corner of UI. The Popup panel may be used to open Control panels (in
addition to the Workset) and to add/remove/rename items in the Workset.
The Message window shows messages regarding the current state of the microscope. The messages span a wide
spectrum, from simple notifications to critical errors. Specific prompts are also sent to this window, in cases where
additional information is necessary to continue microscope operation; for example, specifying the specimen-holder
type when inserting a sample. Be sure to confirm your choice/action using the enter button at the right of the Message
window.
General note: One can use the function key F1 to invoke the UI help pages from any Control panel. Position the
cursor over a particular item and press F1. The relevant help pages for that item or Control panel will automatically
pop up.
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Overview of common Control panels in the UI.
Setup tab. The Control panels in this tab provide information on (and control over) physical
conditions of the microscope: vacuum, high voltage (HT), FEG, aperture, etc. Individual Control
panels may also be called from the Popup panel.





The Vacuum Control panel shows the vacuum level in the different parts of
the microscope: gun, column (octagon) etc. Vacuum is very critical for this
instrument, because of the FEG (Field Emission Gun). The Column Valves
must be closed if microscope is not in use or if the vacuum reading in the
Octagon is higher than 20 Log. Yellow color of the button indicates that the
operation (Valves closed) is performing, gray indicates that the
function/device is not in operation. When the Col. Valves Closed button is
yellow, the column valves are closed. Clicking this button makes it turn grey,
indicating that the column valves are open.





Correct settings for the FEG are critical for optimal Titan performance. At
300kV, Extraction voltage =4300 V, gun lens =3. When the Operate button is
yellow, it indicates that the FEG is Operating. Likewise, when the High Tension
button is yellow, the high voltage is turned on.









The Titan may operate in a range of HT from 80 to 300 kV. Every voltage
requires complete alignment of the microscopes optical system. At EICN, the
microscope is only aligned for 80 and 300 kV. Therefore, there are only two
voltages currently available: 80 and 300 kV.





Apertures in Titan are motorized and controlled via this interface. Choose the
size and mark the appropriate box to insert the aperture:

To center check Center and use the MF knobs to center. Uncheck Center
when done. The larger the C2 aperture, the brighter the beam. 150 m is the
largest Condenser 2 (C2) aperture. The most common settings are 50 m for C1
and 100 m for C2. For HRTEM, the objective aperture usually is not used.
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Vacuum Overview panel.


This Control panel may be accessed
only from the Popup panel (bottom-right
corner of the UI). It shows the Titans
vacuum diagram. Different colors
represent different qualities of the
vacuum: cyan represents good vacuum
for the specific component highlighted
with that color. For instance, in the case
of the FEG, it corresponds to the ultra-
high-vacuum essential for the proper
operation of this component.

Abbreviations:
IGP Ion-Getter Pump; TMP Turbo-
Molecular Pump;

Valve in closed position.



Valve in opened position.













Note: Certain events are not displayed in the current version of this diagram. In particular, the
cartoons of the gun and projection chamber valves do not change according to the open/closed
state of these components. The state of these valves is reported on the Vacuum Control panel (see
above).
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Stage tab.
On this picture, Stage
2
is shown in the flap-out configuration.




This panel controls the Titans CompuStage. On
the left side is the representation of the specimen.
Click on Add to save the current X-Y position of
the stage. Click on Go to recall a previously
saved position. On the right side - Control:
Stage control Power step (adjusts speed of
stage movement); Reset zeroes the XYZ
positions and AB tilt angles of the CompuStage.
It is a good idea to reset the holder (Reset
Holder) before starting work and when you
have finished. Alternatively, it is possible to reset
just XY or tilt (A/B). Wobbler is used for Z-
height adjustment when a new sample is
introduced.








Note: The button turns yellow when wobbler is on:
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Alignment tab.
The Titan is a high-resolution electron microscope. Because of hysteresis of the magnetic lenses,
the microscope needs to be aligned from time to time during its operation. Therefore, it is
expected that users are capable of performing alignments appropriate for their tasks.

There are two different panels in the Alignment tab: Alignments (Procedure Alignment) and
Direct Alignments. The Procedure Alignments are only performed when the microscope is
seriously misaligned. The Direct Alignments are usually performed at the beginning of each
microscope session.





Alignments (Procedure Alignments). Each folder contains several alignment
procedures. Every Procedure contains a sequence of manipulations that must
be completed. In the flap-out, there is a File option where user may
load/upload saved microscope alignment files. If there is serious
misalignment, it may be helpful to reload the standard Titan alignment file
from File. User may also save his/her best alignment in a separate file for
future use. Note: set C2 aperture to 50 m before loading the file (bug in
UI); you may change aperture size later.




These buttons go to the next or previous step in Procedure Alignment.
Do not forget to hit Done, after each step.


In this window, the computer will guide you through Procedure Alignment.
Read carefully and follow the directions.







Direct Alignments. These are the common alignments done during the TEM
session. The Gun Tilt/Shift, Beam tilt pp X/Y, Beam shift, and Rotational
center must be checked often. Fine alignment is necessary for the best TEM
performance. Select alignment from the list, then use MF knobs to adjust
alignment and click Done when done. Each alignment may be performed
independently and many times. These alignments will be saved only if the
user chooses save changes when exiting the UI.


Note: For additional information, please refer to the Direct Alignments Quick
Guide by Agustin Avila-Sakar (FEI Company), located in a laminated sheet
by the microscope.

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Loading the specimen into the holder.
For those who have had previous experience with J EOL microscopes, the Titan holder will feel
very fragile and delicate. Please pay special attention when handling the FEI holders they ARE
really fragile and delicate! Before using, inspect the holder: check the O-ring for cracks or dust. It
must be clean. Check the conical area next to the O-ring it must be clean and without visual
scratches, etc. Do not touch any part of the specimen holder beyond the O-ring. The oil from your
fingers will contaminate the vacuum as well as your sample. Inspect the specimen-holding
mechanism; make sure it is not damaged. Please report any problem immediately! Users are
responsible for any damage to the holder.

Single-tilt specimen-holder.
























Loading the specimen.
There is a special tool to open the clamp, which holds the specimen in the carrier. In order to
open the clamp, (1) locate the small hole at the base of the clamp. (2) Insert the tool into the hole
and slowly move the clamp up into a vertical position (make sure the clamp is secured in this
position). Do not apply excessive force! (3) When clamp is in the vertical position, load the
specimen into the carrier; make sure it is centered well and slowly move clamp down into the
closed position. Control this movement with the tool. Do not remove the tool from the hole unless
clamp is completely closed. The orientation of the specimen should be with the sample face down,
since the holder undergoes a ~140 degree rotation upon insertion into the column (see next
section). Do not use tweezers etc. to manipulate the clamp mechanism. Improper operation will
damage the mechanism.
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Double-tilt specimen-holder (DTSH).

To load the specimen into the holder you need special tools, which you can find in a small plastic
container inside of the plastic bag. These tools are the anti-twist washer, hexring, and exchange
tool. Keep in mind that the hexring is made of Be and it is very expensive piece which can be
easily lost if special attention is not paid. Users are responsible for its replacement in case of loss
due to negligence!


For your
convenience you
can use the loading
station, which is
equipped with the
light, magnifying
lens and vacuum
tweezers.



Procedure for loading specimen.

First, remove plastic cover from the
tip of DTSH. Using vacuum
tweezers place your sample inside
the cup of DTSH.







Put anti-twist washer on top of the
sample making sure that both pins on
the anti-twist washer go into special
notches made in the cup.









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Place hexring on a flat clean surface, covered with
filter paper. Make sure that its wider side is facing up.
Grab it with exchange tool, transfer it to the DTSH
cup and carefully screw it in (clockwise direction).
Dont apply extensive force while screwing the
hexring. Note: There is only one turn of thread in the
cup before screwing hexring in, make sure that
thread in the cup and screw of the hexring are
correctly aligned.


Verify that the top of the
hexring is at the same level as
the top of the cup. The
orientation of the specimen
should be with the sample face
down, since the holder
undergoes a ~140 degree
rotation upon insertion into the
column (see next section). Do
not use tweezers etc. to
manipulate the specimen-
holding mechanism mechanism. Improper operation will damage the mechanism.

Turn the holder 180 to flip the cup up side down and make sure specimen is held in place, though
do it while keeping holder above the desk/filtering paper. Keep in mind that it is not a big deal if
your sample drops at this point, but it will be a lot of trouble if you lose your sample, anti-twist
washer, or the hexring inside the column of the microscope.
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Insertion of Specimen-holder into the microscope column.

1) Load the specimen in the holder as described above. Make sure the
specimen is properly fastened in the holder. Check that the O-ring
and conical surface of the holder are clean and intact.
2) Make sure that the Column Valves are closed (Col. Valves Closed
button is yellow).
3) Turn ON turbo-molecular-pump (TMP) by clicking Turbo on.
The color of the button will first change from grey to orange, then
to yellow. Once it is yellow, the TMP is ready.



4) Locate the small pin on the end of the holder closer
to the tip. Carefully insert the holder into the
CompuStage with the small pin on the holder in the
5 oclock position (large pin at the handle in 11-
oclock position). The pre-pumping cycle will
initiate and the red indicator light will come on.
Note: If double-tilt sample-holder is used, plug
holder connector to the CompuStage. In the
Message window, select double-tilt holder and click
enter button:

5) When the red light goes off (2-5 minutes the
remaining time may be checked in Vacuum
Overview - Popup panel), rotate the specimen-
holder counterclockwise until it stops. Then guide
the holder into the microscope carefully as it is
sucked into the vacuum of the column.

6) Turn off the TMP by clicking Turbo on button (it
will turn grey).


7) Check the vacuum level in Octagon (Workset Setup Vacuum).

It should be 20 log or less:

Removing specimen holder from the microscope. If double-tilt sample-holder is used, unplug
the holder connector from the CompuStage, gently pull out the holder from the column until it
stops, then rotate clockwise to the stop and carefully remove from the CompuStage with two hands
(as was shown in training).

General note: Do not apply any lateral and/or excessive force to the specimen-holder during
insertion or removal!
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Step-by-step Instruction for microscope use

1. Fill up the Dewar flask with liquid nitrogen and install in place, as shown during microscope
training. If the Cold Trap was at room temperature, you may need to allow it to cool for at least
30 minutes. Re-fill liquid nitrogen during the session if needed.

2. Sign in to the logbook.

3. Start the Titan TEM User Interface (UI):

a) Log on to the Titan computer using your username and password.
b) Open User Interface (UI) from Windows quick launch toolbar or from start menu.
Microscope Control-TEM1 will pop up.
c) Workset Setup FEG Control (User). Make sure that FEG Control
parameters are set correctly: HT=300kV; Extraction voltage=4300V and Gun lens
setting (GL) is 3. If you need to change the extraction voltage value, set the value first
and then click the enter button next to the value.
d) Workset Setup Vacuum. Check vacuum in the system: Gun vacuum should
always be at 1; Octagon (column) vacuum should be below 20 log. Verify that Col.
Valves Closed button is yellow (valves are closed). The column valves should always
be closed if the Octagon vacuum is greater than 20 log or when microscope is not in
use. The field emission gun will be damaged if the column valves are opened when the
Octagon vacuum is too high. This will result in an extremely costly and time-
consuming repair.
e) The state of the microscopes vacuum system also may be observed in the Vacuum
Overview - Popup panel, right-bottom corner of the UI.

4. Start digital camera controlling software: Digital Micrograph (DM) or/and TIA. Note: TIA
requires DM to be running (start DM before TIA).

5. Insert specimen-holder into the microscope column in accordance with procedure described
above and demonstration during the training session. Improper insertion will cause vacuum
leak and damage to the vital microscope components, IGPs and/or FEG.

6. If Octagon is 20 log or less, open the gun-valve by clicking Col. Valves Closed button. The
button will turn gray and the Setup tab will indicate Status shown: liner opened. If
everything is fine you should see the beam on the screen and microscope is ready for operation.
If sample is blocking the beam move it using the X-Y joystick. Note: When the column valves
are opened, the CompuStage light will turn red. Do not touch the CompuStage or specimen
holder when the red light is on!

7. Set microscope parameters: magnification 5600x, spot size 3-4; aperture: C1 - 50 m and
C2 - 100 m (the most common settings).

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8. Reset the holder: Workset Stage Stage
2
Control Reset Holder. It is a good
habit to reset the holder when starting and ending a microscope session. Also, if there is a
problem controlling the CompuStage, sometimes resetting the holder may fix the problem.

9. Center the beam: Condense the beam to its smallest size using Intensity knob. Center the
beam using multifunction (MF) knobs Beam Shift X & Y.

10. Center the C2 aperture: Spread the beam just beyond the outer circle on the fluorescent screen.
Open aperture control panel (Workset Setup Motorized Apertures). Check the
Center box next to Condenser 2 and use the MF knobs to adjust the position of the C2
aperture. The C2 aperture is centered well when the beam spreads symmetrically around the
center of the screen.

11. If necessary, insert and center objective or/and selected area aperture(s).

12. Adjust the Z-height: Find an easily recognizable feature and position it in the center of the
screen. In Stage Stage
2
flap-out Control click the Wobbler button. The button will
turn yellow and the image will start shifting back and forth. Minimize amplitude of this
movement by pushing one of two Z-axis buttons. Turn Wobbler off and make sure that A&B
are close to 0. Press Eucentric focus-????.

13. Observe image on the screen. Adjust Intensity to spread the beam over the screen.

14. Use Digital Micrograph or TIA to record images with the digital camera.

15. In Digital Micrograph (DM):

a) Microscope Global Microscope Info fill in the Specimen and Operator name,
leave other fields as is.
b) File Global Info Save Numbered - set up directory path where your files will
be saved (File Directory); create rules for File Name (do not use special symbols like
#/ \| % #@); choose the file format, normally Gatan Format) in File Content and
Format. Choose Save Image As for high-resolution, 16-bit images. Save display As
low-resolution, 8-bit option. Note: Save images on Titan STEM support computer- C
support computer on TITANSTEM/users/your directory. Do not save your data on the
Titan computer!
c) Make sure that beam is spread: CCD chip of the digital camera will be damaged by
condensed beam.
d) On right (DM) panel click Camera Inserted to insert the camera.
e) Uncheck Auto Exposure. Set exposure time manually 0.1 sec. Note: Auto Exposure
slows down the cameras readout. Occasionally, this option may be used in case of
difficulties with imaging.
f) Lift up the microscopes big screen (usually, R1 programmable button).
g) Choose Preview or Search in Workset TV/Camera (UI). Alternatively, start
View in Camera View (right panel) in DM. Adjust microscope Intensity, so intensity
indicator in DM is in green zone. To accelerate the cameras refresh rate, use 2x or 4x
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binning (setup icon). Note 1: The CCD chip of the digital camera is very expensive and
sensitive to beam damage. Always keep the intensity of the beam so that the DM
Intensity indicator is in the green zone. Note 2: The digital camera may be controlled
from either the FEI User Interface (CCD/TV Camera) or Digital Micrograph (DM).
In either case, the image will be displayed in DM.
h) Find the area of interest. Adjust magnification; make sure that DM intensity indicator is
in the green zone.
i) Focus the image using the Wobbler button (not the A-wobbler that was used to adjust
the z-height) at magnification range up to 50-80xK. At higher magnification use the
minimal contrast approach or live FFT (Fast Fourier Transform or power
spectrum) in DM: Process Live FFT.
j) If necessary, use Display Control on the DM left panel to adjust brightness/contrast of
the image. The quality of the image may be judged based on the histogram (left panel)
shape: a good histogram has smooth, bell-like shape and symmetrical.
k) Take a picture: Camera Acquire Start Acquire. It is a good idea to use Auto
Exposure option at this time. If you are planning to take many pictures at the same
magnification and under similar illumination conditions you may uncheck Auto
Exposure to accelerate the process of taking pictures. Note: All your pictures will be
named based on information provided in Global Microscope Info: Specimen name.
l) When sample is changed, do not forget to change Specimen name in Microscope
Global Microscope Info. DM will automatically associate typed in Specimen
name with all pictures taken after its the last change.
m) When all pictures have been collected, save them using save numbered (diskette 1-2-
3 icon) option: select the window with the picture and click Save Numbered, close the
window (Ctrl-W), repeat for every picture. All pictures will be saved in the directory
specified in File Global Info Save Numbered. Note: Save images on the Titan
STEM support computer - C support computer on TITANSTEM/users/your directory.
Do not save your data on Titan computer!

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Shutting Down the System.

1. Bring magnification to 5600x.
2. Spread the beam.
3. Reset the holder (Stage Stage
2
open flap-out Reset Holder).
4. Close Digital Micrograph and TIA.
5. Close column valves by clicking Col. Valves Closed button in Setup Vacuum. The
button will turn yellow and the Setup tab will indicate Status shown: liner closed.
6. If you are using the double-tilt holder, disconnect the cable from the CompuStage.
7. Remove the specimen holder from the microscope column.
8. If you are the last person operating the microscope for the day, make sure that you start a
cryo cycle. Otherwise, proceed to the next step.
Cryo cycle procedure: (1) remove the liquid nitrogen dewar from the cold trap as shown
during the training session; (2). Open Vacuum tab on the Workset. Open its flap-out. Click
Cryo Cycle On button. The TMP will start its operation and the Cryo Cycle On button will
turn yellow. Note: If you are the last user of the day, dont leave before starting a cryo cycle.
9. Close UI window.
10. Log off from Titan computer.
11. Complete the record in the logbook.

M Ma an ny y t th ha an nk ks s f fo or r f fo ol ll lo ow wi in ng g t th he es se e i in ns st tr ru uc ct ti io on ns s! !

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Appendix:


Basic Alignments.

All alignments except astigmatism are accessible via the Direct Alignments Control panel in the
Workset or from the popup panel.

1. Gun tilt alignment. Click Gun Tilt in the Direct Alignments. Using MF, adjust intensity
of the beam to its maximum. Click Done button.
2. Gun shift alignment. Use L3 programmable button to set the spot size to 3. Condense the
beam. Select Gun shift. UseMF knobs to bring the beam to the center of the screen.
Switch to the spot size 9 (R3 programmable button). Condense the beam. Select Align
beam shift. Use MF knobs to bring the beam to the center of the screen. Repeat until beam
is in the center for both spotsizes 3 and 9.
3. Beam tilt pivot point X and Y alignment. Click Beam tilt pp X in the Direct Alignments.
The beam will begin to wobble. Using MF knobs, stop beam wobbling, so that beam is
stationary in the center of the screen. Click Done button. Select Beam tilt pp Y in Direct
Alignments. Repeat the above procedure for the Y pivot points.
4. Rotational center alignment. Perform this alignment on a visible feature on the sample. Use
high magnification for this alignment. Select Rotation center alignment in the Direct
Alignments. Image of the feature will start moving. Use MF knobs to minimize the
movement. Click Done button.
5. Astigmatism. Select Stigmators at popup panel (right-bottom corner of the UI). Choose
Condenser, Objective or Diffraction. Use the multifunction (MF) knobs to do the
correction. For the condenser, adjust the beam shape to become a circle. For the
objective, make the granularity of a high magnification image isotropic (use CCD +live
FFT for optimal results). For diffraction, make the central spot of the defocused diffraction
pattern circular.

For additional information, please refer to the Direct Alignments Quick Guide by Agustin Avila-
Sakar (FEI Company), located in a laminated sheet by the microscope.

By Sergey Ryazantsev
Ray Bergstrom
Sergey Prikhodko
Ivo Atanasov
Agustin Avila-Sakar (FEI Company)
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all rights reserved, September-October 2008